Application of serofoi package to Fiji dengue seroprevalence data

serofoi_fiji.R

# serofoi analysis on Fiji serosurvey data

# Load libraries
library(remotes)
remotes::install_github("TRACE-LAC/serofoi")
library(serofoi)
library(rio)

# Load Fiji dengue data
url_fiji <- "https://raw.githubusercontent.com/adamkucharski/fiji-denv3-2014/master/data/serology_inputs.csv"
data_fiji <- rio::import(file = url_fiji)

# Format Fiji data - DENV3 positive in 2013 (2015 = DENV3BP)
data_tally <- data_fiji |> group_by(AGE_2015) |> summarise(pos=sum(DENV3BP),tot=n())

# Loading and preparing data for modelling
serodata <- data.frame(age_min=data_tally$AGE_2015, # min age
                            age_max=(data_tally$AGE_2015+4), #max age
                            counts=data_tally$pos, # positive for DENV serotype
                            total=data_tally$tot, # total tested
                            tsur=2015, # year of survey
                       survey = "Fiji",
                       country = "FJI",
                       test="MIA",
                       antibody="IgG"
                  )

# Example from package
# data("serodata")
serodata_test <- prepare_serodata(serodata)

# Model implementation
model_epidemic <- run_seromodel(serodata = serodata_test,
                                foi_model = "tv_normal_log",
                                n_iters = 500)

# Visualisation
#plot_seromodel(model_epidemic, size_text = 6)
plot(model_epidemic$foi_cent_est$year,model_epidemic$foi_cent_est$medianv)